DNA sequencing data in MDS-patients treated with allogeneic transplantation

SND-ID: 2023-289. Version: 1. DOI: https://doi.org/10.48723/0k7w-2k05

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Associated documentation

README.txt (1.5 KB)

Sequence Alignment Map Format Specification_The SAM_BAM Format Specification Working Group May 2023.pdf (533.65 KB)

Citation

Creator/Principal investigator(s)

Tetsuichi Yoshizato - Karolinska Institutet, Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)

Sten Eirik Jacobsen - Karolinska Institutet, Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)

Research principal

Karolinska Institutet - Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)

Description

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).

Data contains personal data

Yes

Sensitive personal data

Yes

Type of personal data

Genetic data

Code key exists

Yes

Language

English

Method and outcome

Unit of analysis

Individual/Patient

Population

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

Study design

Experimental study

Preclinical study

Sampling procedure

Non-probability

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.

Biobank is connected to the study

This study has used existing samples from a scientific collection or biobank

Scientific collection or biobank name: Karolinska Institutet MDS biobank

Type(s) of sample: Bone marrow cells

Number of individuals/objects

Data format / data structure

Text

Data collection

Geographic coverage

Administrative information

Responsible department/unit

Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)

Ethics Review

Ref. 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

Topic and keywords

Research area

Medical and health sciences (Standard för svensk indelning av forskningsämnen 2011)

Hematology (Standard för svensk indelning av forskningsämnen 2011)

Cancer and oncology (Standard för svensk indelning av forskningsämnen 2011)

Keywords

Hematopoietic stem cells, Hematopoietic stem cell transplantation, Myelodysplastic syndromes

Publications

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.
DOI: https://doi.org/10.1182/blood.2023022851

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