NBDC Research ID: hum0527.v1
SUMMARY
Aims: Follicle center lymphoma (FCL) of the lower female genital tract (LFGT) is a rare lymphoma, with fewer than 20 cases reported to date. Since the genetic features of FCL of the LFGT have not been well characterized, we aimed to identify genetic alterations in this tumor through whole-exome sequencing and targeted gene panel analyses.
Methods: Whole exome sequencing analysis
Participants/Materials: FCL of the LFGT: 1 case
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000823 | NGS (Exome) | Controlled-access (Type I) | 2025/08/05 |
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MOLECULAR DATA
| Participants/Materials |
FCL of the LFGT (ICD10: C82.9): 1 case a frozen tumor tissue obtained from a surgically resected uterine cervical tumor: 1 sample |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq X Plus] |
| Library Source | DNAs extracted from a frozen tumor tissue |
| 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-MEM (v0.7.17-r1188) |
| Mapping Quality | Mapping rate 99.97% |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | 158 bp |
| Filtering (QC) | Quality control was performed using FastQC, trimming with Trimmomatic, duplicate removal with Picard, and variant filtering with GATK FilterMutectCalls. |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000965 |
| Total Data Volume | 3.7 GB (fastq, vcf) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takumi Kitaoka
Affiliation: Department of Pathology, Yonezawa City Hospital
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | The specific mechanism of fibrosis in IgG4-related sialadenitis | 22K09661 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
