NBDC Research ID: hum0439.v1
SUMMARY
Aims: Familial hypercholesterolemia (FH) is an inherited disorder caused by mutations in the low-density lipoprotein (LDL) receptor-related gene. FH patients have a significantly increased LDL-C compared to non-genetic hypercholesterolemia, the progression of atherosclerosis is more rapid, and the associated organ damage is more severe. FH heterozygotes are found in more than 1 in 500 people and homozygotes are found in more than 1 in 1 million people, and the total number of FH patients in Japan is estimated to be more than 250,000. Among various inherited metabolic diseases, FH is one of the most frequent and frequently encountered diseases in daily medical practice, but patients heterozygous for FH are not always correctly diagnosed. Therefore, we decided to perform genetic testing in the diagnosis of FH.
Methods: For the LDLR and PCSK9 genes, the genome is cut out using the CRISPR-Cas method, and only that portion is analyzed using a nanopore sequencer.
Participants/Materials: Genome sequence information from nanopore sequencing of LDLR and PCSK9 genes in 5 FH patients and 1 control
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| DRA017996 | NGS (Target Capture) | Unrestricted-access | 2024/02/27 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
FH (ICD10: E780): 5 cases 1 Control |
| Targets | Target Capture |
| Target Loci for Capture Methods |
LDLR (Low-Density Lipoprotein Receptor): Chr19: 11089463-11133820 PCSK9 (Proprotein Convertase Subtilisin/Kexin Type 9): Chr1: 55039548-55064852 * LDLR and PCSK9 genes were selectively excised from the entire genome using CRISPR-Cas9, followed by ligating sequencing adapters for targeted sequencing. The background DNA remains unremoved, which results in a small amount of reads from random regions. |
| Platform | Nanopore [MinION] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Cas9 Sequencing Kit (SQK-CS9109) |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
LDLR location: read length up to 46.2 kb PCSK9 location: read length up to 26.5 kb |
| DDBJ Sequence Read Archive ID | DRA017996 |
| Total Data Volume | 5.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Koh Ono
Affiliation: Department of Cardiovascular Medicine, Kyoto 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) | Elucidation of the functions of long non-coding RNA in cardiovascular diseases | JP20H03675 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | CRISPR-Cas9-guided amplification-free genomic diagnosis for familial hypercholesterolemia using nanopore sequencing. | In submission | DRA017996 |
| 2 |
