NBDC Research ID: hum0305.v1
SUMMARY
Aims: Subsequent solid cancers after allogenic hematopoietic cell transplantation may have unique genomic profiles compared with de novo cancers. In order to identify such profiles, we applied whole exome sequencing (WES) of subsequent solid cancers after allogeneic hematopoietic cell transplantation as well as de novo cancers.
Methods: Genomic DNA was extracted using a QIAamp Fast DNA Tissue kit, GeneRead DNA FFPE kit or QIAamp DNA Mini kit. Libraries for WES were prepared using the Twist library preparation kit. The libraries were sequenced using a Novaseq 6000 or DNBSEQ G400 with the paired-end option.
Participants/Materials: 14 fresh-frozen tumor tissues and 14 formalin-fixed-paraffin-embedded (FFPE) tumor tissues of 14 de novo cancer patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000377 | NGS (Exome) | Controlled-access (Type I) | 2021/11/29 |
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MOLECULAR DATA
| Participants/Materials |
de novo cancer (tongue cancer [ICD10: C02.9], colon cancer [ICD10: C18.9]): 14 cases fresh-frozen tumor tissue: 14 samples, FFPE tumor tissue: 14 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [NovaSeq 6000] MGI [DNBSEQ-G400] |
| Library Source | DNAs extracted from fresh-frozen and FFPE tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Twist library preparation kit |
| Fragmentation Methods | Enzymatic Fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000491 |
| Total Data Volume | 288.4 GB (bam) |
| Comments (Policies) | NBDC policy and Company User Limit |
DATA PROVIDER
Principal Investigator: Yoshihiro Inamoto
Affiliation: Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital
Project / Group Name: Comprehensive molecular profiling of subsequent solid cancers after allogenic hematopoietic cell transplantation
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Establishment of personalized medicine for secondary solid tumors after hematopoietic cell transplantation based on genomic characterization | JP20ck0106539 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | MicroSEC filters sequence errors for formalin-fixed and paraffin-embedded samples | doi: 10.1038/s42003-021-02930-4 | JGAD000491 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
