NBDC Research ID: hum0289.v1
SUMMARY
Aims: Disease relapse is a major cause of treatment failure after allogeneic hematopoietic cell transplantation (HCT), and mechanisms on relapse still remain to be elucidated. We experienced a patient with chronic myelomonocytic leukemia (CMML) who underwent haploidentical HCT from his daughter and developed relapse. To understand the mechanisms on relapse after HCT, we analyze blood samples at HCT and at relapse.
Methods: We analyzed peripheral blood samples that had been collected at HCT and relapse. CD14+/CD16- monocytes that accumulate typically in CMML were isolated by flow cytometry. Whole-exome sequencing, RNA sequencing, and methylation array were performed to determine the mechanism of relapse.
Participants/Materials: chronic myelomonocytic leukemia (CMML): 1 case; peripheral blood samples that had been collected at allogeneic hematopoietic cell transplantation and relapse (2 samples)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000317 | Controlled-access (Type I) | 2022/09/09 |
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MOLECULAR DATA
| Participants/Materials |
chronic myelomonocytic leukemia (CMML) (ICD10: C93.1): 1 case (2 samples) peripheral blood samples collected at HCT and relapse |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CD14+/CD16- monocytes isolated from peripheral blood samples |
| Cell Lines | - |
| Library Construction (kit name) | SMART-seq Stranded kit |
| Fragmentation Methods | SMART-seq Stranded kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| QC |
NovaSeq Control Software v1.6.0 Real Time Analysis (RTA) v3.4.4 bcl2fastq2 v2.20 |
| Mapping Methods |
Genedata Profiler Genome 13.0.11 STAR 2.6.0c |
| Coverage (Depth) | 76.3-84.1% |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000428 |
| Total Data Volume | 23.9 GB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
chronic myelomonocytic leukemia (CMML) (ICD10: C93.1): 1 case (2 samples) peripheral blood samples collected at HCT and relapse |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from CD14+/CD16- monocytes isolated from peripheral blood samples |
| Cell Lines | - |
| Library Construction (kit name) | SureSelectXT Reagent kit, SureSelectXT Human All Exon kit V6 (Agilent Technology) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| QC |
NovaSeq Control Software v1.6.0 Real Time Analysis (RTA) v3.4.4 bcl2fastq2 v2.20 |
| Mapping Methods |
DRAGEN Bio-IT Platform 3.5.7 SnpEff v4.2 VCFtools 0.1.9 |
| Coverage (Depth) | >99% |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000428 |
| Total Data Volume | 23.9 GB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
chronic myelomonocytic leukemia (CMML) (ICD10: C93.1): 1 case (2 samples) peripheral blood samples collected at HCT and relapse |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium MethylationEPIC BeadChip Kit] |
| Library Source | DNAs extracted from CD14+/CD16- monocytes isolated from peripheral blood samples |
| Cell Lines | - |
| Library Construction (kit name) | Infinium MethylationEPIC BeadChip |
| Algorithms for Calculating Methylation-rate (software) |
iScan System 309171 Rev B iScan Control Software 3.4.8 |
| Filtering Methods |
GenomeStudio Software V2011.1 Methylation Module 1.9.0 |
| Normalization of microarray |
GenomeStudio Software V2011.1 Methylation Module 1.9.0 |
| Probe Number | 850,000 probes (Infinium MethylationEPIC BeadChip) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000428 |
| Total Data Volume | 23.9 GB (bpm) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yu Akahoshi
Affiliation: Saitama Medical Center, Jichi Medical University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Emergence of clone with PHF6 nonsense mutation in chronic myelomonocytic leukemia at relapse after allogeneic HCT | doi: 10.1007/s12185-021-03284-7 | JGAD000428 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
