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DNA sequencing data in MDS-patients treated with allogeneic transplantation

https://doi.org/10.48723/0k7w-2k05
The deposited data consists of 47 bam files for targeted DNA sequencing and somatic mutation list called by bulk whole-genome sequencing in patients with myelodysplastic syndromes or related myeloid malignancies who received allogeneic stem cell transplantation. The objective of this data collection was to assess whether somatic mutation can be a marker for detecting early relapse. DNA sequencing was performed to identify somatic mutation candidates using samples collected at diagnosis and also performed for the comparison of the sensitivity of detection between digital droplet PCR and next-generation sequencing. We used three different gene panels for targeted DNA sequencing and the gene lists can be found in the cited Blood paper. Read alignment was performed against the GRCh37. In two patients in whom no recurrent driver mutations were identified, whole genome sequencing was performed. After alignment to GRCh37, somatic mutations were called using Genomon2, and identified somatic mutation list was deposited. The total size of the deposited data is approximately 25 GB (24586652781 bytes).
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Documentation files

  • README.txt
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  • Sequence Alignment Map Format Specification_The SAM_BAM Format Specification Working Group May 2023.pdf
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Citation and access

Data access level:

Creator/​Principal investigator(s):

Research principal:

Data contains personal data:

Yes

Type of personal data:

Genetic data

Code key exists:

Yes

Sensitive personal data:

Yes

Citation:

License:

Language:

Method and outcome

Unit of analysis:

Population:

Patients with myelodysplastic syndromes or related myeloid malignancies received allogeneic stem cell transplantation.

Study design:

  • Experimental study
  • Preclinical study

Sampling procedure:

Description of sampling:

Patients with myelodysplastic syndromes (MDS) and related myeloid malignancies diagnosed according to World Health Organization (WHO) 2016 classifications that had undergone allogeneic hematopoietic stem cell transplantation (allo-HSCT) at Karolinska University Hospital were included in the study. All samples were collected after informed consent and analyzed according to ethical approval and the Declaration of Helsinki. Patients were grouped into relapses and continuous-complete remission without signs of relapse ≥66 months after allo-HSCT.

Number of individuals/​objects:

27

Data format/​data structure:

Samples/material Existing from scientific collection/biobank

Name:

Karolinska Institutet MDS biobank

Type(s) of sample:

Bone marrow cells

Administrative information

Responsible department/​unit:

Department of Medicine, Huddinge [H7]

Ethics Review:

- EPN 2017/1090-31/4

Ethical review: Studier av ärftliga och förvärvade sjukdomsmekanismer vid myelodysplastiskt och myelodysplastiskt / myeloproliferativt syndrom, MDS-relaterad AML samt angränsande hematologiska tillstånd med behov av förbättrad differentialdiagnostik

Funding

Funding agency:

Award number:

2023-02061_VR

Award title:

Role of Stem Cells in Normal and Malignant Hematopoiesis

Funding information:

Although insults to the blood-forming system highlight the need for more rapid blood replenishment from hematopoietic stem cells (HSCs), existing models of hematopoiesis implicate only one, mandatory, differentiation pathway for each blood lineage. We have evidence for non-hierarchical relationships between mouse HSCs replenishing all blood lineages and exclusively platelets through distinct pathways. We will investigate the role of these 2 pathways and the replenished platelets at different stages of ontogeny and in response to different challenges, using single HSC transplantations, genetic fate mapping and single cell RNA sequencing, with the goal of providing a platform for combatting transplantation-and drug-induced thrombocytopenia. It remains unclear to what degree the extensive steady-state turn-over of blood cells can progress in absence of HSCs, a question with important implications also for the cancer stem cell hypothesis, implying that efficient therapeutic targeting of the malignant stem cells might be sufficient to eliminate the entire malignancy. No studies have addressed this following efficient and selective elimination of stem cells in vivo. Herein we aim to  engineer T cell receptors (TCRs) that efficiently and specifically target antigens selectively and highly expressed on normal and malignant HSCs to establish if elimination of the rare malignant stem cells is not only required, but potentially sufficient for a cure.

Topic and keywords

Standard för svensk indelning av forskningsämnen 2025:

Keywords:

Publications

Citation:

Dimitriou M, Mortera-Blanco T, Tobiasson M, Mazzi S, Lehander M, Högstrand K, Karimi M, Walldin G, Jansson M, Vonlanthen S, Ljungman P, Langemeijer SMC, Yoshizato T, Hellstrom-Lindberg ES, Woll PS, Jacobsen SEW. Identification and surveillance of rare relapse-initiating stem cells during complete remission post-transplantation. Blood. 2023 Dec 14:blood.2023022851. doi: 10.1182/blood.2023022851.

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Metadata

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