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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.

Research ID

hum0612-v1Release info

Latest

Research title

Registered research projects for new genetic test analysis data in the restricted-access database

Research overview

Aims
The current genetic testing methods are exon capture sequencing and MLPA and limited to detecting point mutations in exons, as well as copy number of exons. We have developed and published papers on novel testing methods, such as vLAS (very long amplicon sequencing), rLAS (RNA long amplicon sequencing) and TgCap (targeted genome capture sequencing), which can detect structural abnormalities, deep intronic and mosaic variants. This study aims to ensure that personal information is handled appropriately when reporting cases with new findings or the development of new genetic testing methods. To this end, we will register these data with the NBDC Human Database for restricted access, thereby facilitating verification and secondary use by other researchers.
Methods
vLAS: We amplified peripheral blood DNA using a long PCR set of approximately 20 kb, which covered the entire genomic region, including the introns of the target gene. The amplicons were then pooled and libraries were prepared using Nextera (Illumina), after which they were sequenced on a MiSeq (Illumina).

rLAS: Peripheral mononuclear cells were isolated from whole blood. Total RNA was extracted using Trizol and single-stranded cDNA was synthesized using oligo-dT primers. The full-length mRNA of the ERCC4 gene was then amplified by Long RT-PCR using this as a template. A library was constructed from the amplification products using Nextera (Illumina) technology, and the library was sequenced on a MiSeq (Illumina).

The variant was identified using vLAS on peripheral blood DNA. The splicing abnormality was quantitatively analyzed using rLAS on total RNA from peripheral mononuclear cells.
Participants/materials
Xeroderma pigmentosum: 1 case (one vLAS specimen and one rLAS specimen)
A novel splicing variant, NC_000016.10(NM_005236.3):c.207+196T>A, was identified in a deep intron of the ERCC4 gene and the patient was diagnosed with type F.
URL

Datasets

CartDataset IDType of dataAnalysis methodAccess criteriaDate published
JGAD001129NGS (Targeted DNA-seq, Targeted RNA-seq)
  • vLAS (very long amplicon sequencing)
  • rLAS (RNA long amplicon sequencing)
Controlled-access (Type I)

Data provider

Principal investigator
Yo Niida
Affiliation
Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University

Research projects

No research projects.

Grants

NameTitleProject number
Kanazawa Medical University
NA
  • 11181
  • 26699

Related publications

TitleDOIDataset ID
A case with Xeroderma Pigmentosum Type F manifested a mild phenotype due to a deep intronic variant of the ERCC4 gene
https://doi.org/10.3389/jcia.2026.16180 (opens in a new tab)

Controlled access users

No use of the controlled access data has been recorded.